Advancement of Precision Medicine Through the Study of SNPs

Researchers from the National Institute of Environmental Health Sciences (NIEHS) led by Shephard Schulman, M.D., and Stravros Garantziotis, M.D., conducted a study that examined genetic variation in the asthmatic population, and how these variations effect each individual's response to the environment, specifically, air pollution. For their study, Schulman and Stravros were able to gather 2,704 volunteers, who had varying degrees of asthma, through a DNA bank. Schulman explained that these degrees exist, because of a specific type of genetic variation termed single nucleotide polymorphism or SNP, which he states, "can alter the way proteins are made and make individuals more or less prone to illness" (1).  

The two lead researchers isolated four SNPs of interest, and set their study by dividing the participants into three groups according to the SNP data: those who were highly sensitive to air pollution, those who were insensitive, and those in between. With the subcategories of genetic variation in place, the research team used participants' addresses and their distance from a major highway to determine air pollution effect, since air pollution is generally higher in places located near these highways. 

As a result of the study, the researchers found that those who had the SNP that dictated hyper-sensivity and lived near a major highway had severe symptoms related to asthma, while those who were insensitive and did not live near a major highway showed less severe symptoms. With the conclusion of this study, the researchers hope to advance the field of precision medicine. Precision medicine focuses on preventative treatment specific to an individual. 

For me, this study sheds light on how vital genetics can be on disease prevention. If an individual is known to have a genetic variation that leaves them prone to certain illnesses aggravated by the environment, a systematic approach can be taken in finding a specific treatment to aid the individual. Instead of spending money on costly prescriptions, a better approach may be to tailor/adjust that person's lifestyle to the environment they live in. In the case of those who are hyper sensitive and live near major highways, installing an air filter may be the first step in the right direction.  

Resource
https://www.sciencedaily.com/releases/2018/08/180831130117.htm

Additional Resources
https://www.sciencedaily.com/releases/2016/09/160904181251.htm
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3984232/

New Genetic Markers Can Indicate Lifespan

New Genetic Markers Can Indicate Lifespan



Researchers from the Swiss Institute of Biochemistry, the Lausanne University Hospital, the University of Lausanne, and the EPFL have identified 16 genetic markers associated with a decreased lifespan. About 10% of the population has some configuration of these markers. Changes in locations in an individual’s DNA sequence, like single-nucleotide polymorphisms(SNPs), could affect lifespan. When indicating genes, the researchers prioritized changes in the DNA which are known to be linked to age-related disease. Three genes could act as biomarkers for an increase of lifespan are RBM6, SULT1A1 and CHRNA5 lower brain expression of three genes neighboring the SNP. This article is interesting because it indicates a way for scientist to calculate lifespans. This idea brings up the moral/ethical questions should scientist look into individual’s lifespan and if scientist can calculate lifespan should individuals be informed of their approximate lifespans?

The Genetics of Blonde Hair

Scientists have found that replacing of the DNA’s four letter  is the key  to genome shift a particular gene’s activity and that leads it to fairer in hair color. Over the time past six years  studies of genetic variation  in thousands of people have linked atleast eight DNA regions that heightened  basis of the blondness in people’s hair. Some of the base changes in the DNA letter  or single nucleotides  were in genes that involve in the production of pigment in someone’s skin and hair.The changes in the regulatory DNA could result in hair color not skin color change because regulatory DNA can change gene activity just in  certain parts of the body that is why if your hair changes color your skin will not and vice versa. The article  goes on say how in Northern Europeans the KITLG a single nucleotide polymorphism   was i strongly linked to blondness because it codes for a protein of specialized for it . The single nucleotide polymorphism had caught the eye of geneticist David Kingsley and he found this applies to fish, mice   as it does to humans.  There is a switch that regulates the of KITLG  which easier  to predict red and black color accurately based on the hair color related SNPS but it is harder to the blonde and brunettes. I liked reading this article because I learned that the genetic cause  and how the evolution occurred. The KITLG is active in many places in the body and now I know why many people have blonde hair instead of another hair color and how the effect of KITLG is specific to hair and not skin or eye color  which is quite unique an fascinating  compared the most pigmentation genes today which is what I had not expected at all before.

http://www.sciencemag.org/news/2014/06/genetics-blond-hairhttps://news.nationalgeographic.com/news/2014/06/140601-blond-hair-color-gene-mutation-science/

Lung Cancer Biomarkers Identified

An article on Science Daily states the new findings of Yafang Li and researchers at Dartmouth college. They have identified three new lung cancer biomarkers. There are two causes behind lung cancer, the environment and genes. It is well known that smoking causes lung cancer but there are actually gene variants that affect a person's susceptibility to smoking. These genes are the culprits behind the development of lung cancer. The biomarkers found are called novel single-nucleotide polymorphisms (SNPs) and they emphasize the vulnerability of developing lung cancer. In other words, a person's smoking behavior, which increases their chance of obtaining lung cancer, is influenced by these three SNPs. An article on Genetic Engineering and Biotechnology News reinforces the findings, showing the p-values in the study that were used to identify the three SNPs.
 
 I believe this new finding is a tremendous step in the treatment for those with lung cancer. As technology advances, research does too, which enables us to better understand certain diseases and come up with an effective plan to cure those diseases. However, the research study was only done in a Caucasian population. Therefore, the genes found might not be the same in other ethnicities. I believe the research team should expand their findings in other populations. The research team is determined to do so and test other populations so more gene-smoking interactions are found.
https://www.sciencedaily.com/releases/2017/10/171028081456.htm
https://www.genengnews.com/gen-news-highlights/novel-lung-cancer-biomarkers-identified/81255101

Closer Links to the Genetics of Fraternal Twins

The chance of having fraternal twins has long been known to increase if relatives have also had the  event occur, however researchers have recently been underway to find a closer link to the explanation. The United States alone saw a 76% increase in the fraternal twin population from 1980 to 2011, and scientists want an answer.

This article explains the path scientists have taken to identify the increasing factor. They've collected and compared single nucleotide polymorphisms (SNPs) of 2000 mothers of fraternal twins to SNPs of mothers who had not had twins. Researchers narrowed the results down to find two SNPs that increase a woman's likelihood of having fraternal twins by about 30%!

One of the SNPs is known to cause an increase in the hormone involved in the production of follicles, which are the sites within the ovaries that house and mature the eggs before they are released from the ovary. If the levels of this hormone is too high, the mother has an increased chance of releasing multiple eggs.

The second SNP is a bit more complicated. This one in particular is a gene that alters the way molecules signal to each other. This gene in turn, called SMAD3, has an affect on the way that the ovaries respond to the hormone coded by the other SNP. This same gene has also been linked to osteoarthritis. Scientists are planning to conduct further research on how mothers react differently due to the SMAD3 gene. These results presented were only the first step.

It's really awesome that this group of scientists have made such progress on identifying the genetic components behind having fraternal twins. This is the closest that scientists have yet to come in relation to this subject matter. This is not exactly the most critical research to be done, as there usually aren't complications or anything wrong with birthing fraternal twins. However its still always great to hear about the evolution of genetic findings in all aspects of life.

Attraction Guided by Our Genes

     We have all heard the common saying "opposites attract," whether it be in elementary school science class or our parents talking to us about relationships.  This theory seems logical; why would you want to be around someone just like you? We are all led to believe that this deems true, but it turns out, it is not. The idea that we attract people who are actually similar to us is known as assortative mating. This includes mating based on age, race, facial characteristics, and body type which all have to do with our genes. Couples tend to seek partners with similar DNA, and this is proven more common than seeking a partner based on socioeconomic status or education level, which was believed prior to this. Researchers studied single nucleotide polymorphisms which is where humans differ in DNA. It was found that married couples were more genetically similar than those chosen at random.

     I find this article very interesting because it is now making me rethink my prior relationships and ones that may friends have been in and are currently in. I have always thought that the saying "opposites attract" rang true, but now that I think about it, my friends and their significant others are very similar. They may differ in certain interests, but when it comes down to it on a more personal level, they are very similar. It's amazing what we can discover with science, and the ideas that researchers come up with are definitely incredible.

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Neurodermatitis Genes Influence Other Allergies

There is a link between the skin condition atopic dermatitis and asthma, and it is tied to specific genetic loci that present a risk. The Max Delbruck Center for Molecular Medicine in the Helmholtz Association, where research was conducted on this disease, found seven genetic risk loci important to both diseases. The data used was collected from over 20,000 people. Atopic dermatitis has existing regions that determine the risk for the disease, which happen to also be the same regions that follow a typical allergic path that leads to asthma. The usual pattern, in which atopic dermatitis forms early in life, followed by food allergies and then asthma, is referred to as the atopic march.

In order to come to a basis for discovering the connected regions, the researchers performed a meta-analysis specific to genome-wide association studies, in which both patients and healthy individuals were compared. Within these bounds, the cases focused on individuals who developed atopic dermatitis and then asthma. The studies were concerned with Single Nucleotide Polymorphisms. Two regions in particular were most of interest, as they demonstrated the greatest connection between atopic dermatitis and asthma. It was not of great surprise that there are connections between allergic diseases, as the same genetic loci that produce certain factors should be able to cause other similar variations. If there are specific genetic loci that are associated with allergic conditions, it would make logical sense that many different expressions could result from the same area.

Being that this was one of the first research studies conducted on atopic dermatitis with a focus on genetic possibilities, it would be interesting if similar research was conducted on other related allergic diseases.

Puzzling Pregnancy Variant

A report published in Science Magazine, and reviewed on TheScientist.com suggests that there is a striking link between mitotic aneuploidy and a nucleotide variant (SNP rs2305957) of chromosome 4 of maternal genomes. What is the significance of this, and what does it all mean? Well, since aneuploidy, or having the incorrect number of chromosomes in a cell, is the most common reason for failed pregnancy, the importance of this discovery is obvious. Not so obvious, however, is the fact that the team doing the study found that this single nucleotide variant's frequency reaches up to 45% in human populations. Coupled with the fact that this variant is completely absent in Neanderthal genomes, this may suggest that positive selection in human evolution has allowed this gene to proliferate.
The question not answered by this study is the purpose of the rs2305957 variant. Dmitri Petrov, a scientific researcher at Stanford University, believes that the variant might have established paternity confusion. This hypothesis suggests that when males were unsure if a child belonged to them, they would care for all of the children equally, benefiting the group as a whole. Whether this, or the many other theories circling this new discovery are true, is unknown. But the fact that evolution allowed a gene variant that reduces the number of successful pregnancies to proliferate, is puzzling to say the least.

Motion Sickness and Genetics

When people think about motion sickness, many do not understand the role that genetics plays with it. In simple terms, motion sickness is a condition that occurs in individuals that experience nausea, vertigo or migraines when traveling in a moving vehicle. It is fairly common--affecting approximately one in three people--and has been shown to have high heritability.

Recently, a genetics company, 23andMe conducted a study involving 80,000 of their customers to understand the genetics of motion sickness. The study found that there are 35 genetic factors associated with motion sickness at the genome-wide significant level. These genetic factors are referred to as single-nucleotide polymorphisms (SNPs).

What was interesting was that most of these SNPs were found in or near genes that are involved eye, ear, balance, and cranial development. Others were found near genes that have a role in the nervous system, glucose homeostasis, or hypoxia. Additionally, the study revealed that SNPs exhibit sex-specific effects--women endured stronger effects (three times more) than men did.The study was also able to conclude that these genes were also linked to other conditions such as migraines, morning sickness, and postoperative nausea and vomiting (PONV).

Since the study indicated that the nervous system plays an important role with motion sickness, it can possibly help researchers understand the genetics of motion sickness better. Possible risk factors and future treatments can be outlined given the results of the study. This would be a wonderful advancement in order to help target the issue underlying motion sickness. Being one that suffers from some mild cases of motion sickness, future research would be very beneficial.

Original article: click here.

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Thousands of Never-Before-Seen Human Genome Variations Uncovered

     A new genome sequencing process known as Single-Molecule, Real-Time sequencing (SMRT) has been developed and used to discover thousands of genetic variants and close numerous mapping gaps in the human genome. Through this sequencing method, it is possible to determine which genetic mutations are responsible for certain conditions, most of which have yet to be discovered. According to what scientists call the “missing heritability problem”, the genetic cause for only about half of the inherited conditions has been determined. However, the main reason for this problem is the fact that the standard methods of genome sequencing are not as precise as SMRT. These methods analyze millions segments of DNA that are approximately 100 bases long and use this information to create a genome map. By looking for the replacement of a single nucleotide base, known as a single-nucleotide polymorphism or SNP, genetic variations in the human genome can be identified.

     Due to the limitations in technology, DNA sequences of 5,000 bases or more were unable to be sequenced using the standard methods of genome sequencing. However, through the use of SMRT, DNA sequences of more than 5,000 base pairs can be analyzed and sequenced. Therefore, through the use of this new sequencing technology, much more detailed genome maps can be created. A study was conducted upon a hydatidiform mole, which is when an egg that lacks the DNA of the mother is fertilized by a sperm and only carries one copy of each gene. Due to this, the search for genetic variation becomes easier when analyzing the hydatidiform genome. It was concluded that 26,079 segments differed from a reference human genome when using the SMRT method, 22,000 of which had never been reported before. 

     I thought this article was interesting because it shows how quickly genome research is advancing and how more detailed maps of the human genome can be used to determine the causes of hereditary conditions. In the future it may be possible to sequence a patient’s genome at the doctor’s office and tell him that the presence of particular SNPs or variations may make him more susceptible to a specific disease. Advances like these will make it easier to not only cure diseases and conditions that occur in the human body, but also prevent them before they arise.

Source: Thousands of Never-Before-Seen Human Genome Variations Uncovered

Genetic Match? People Marry Those With Similar DNA

New research supports the idea that people tend to pick spouses in which their genetic profile is similar to their own. Based on the journal Proceedings of the National Academy of Sciences, mating isn't truly genetically random. Benjamin Domingue from the University of Colorado, analyzed genetic information from 825 non-Hispanic white american and found that married people have more similar DNA segments than random pairs of people. It was found that people tend to marry others who are similar to them in education, social class, race and body weight; this is called assortative effect. The assortative effect based on education was three times stronger than sorting based on genes.

Further research from the LATimes compared 1.7 million single nucleotide polymorphisms and also found that married couples were more genetically similar than random pairs. Even though similarities in genes were found in married couples, it was only one third the magnitude compared to educational similarities found between couples.



Article: http://www.livescience.com/45674-genetic-match-marriage.html

Latinas and Breast Cancer

Studies are uncovering new links from genes to cancer every day. Recently, geneticists unveiled that there may be a new link between a genetic variant, popularly found among Latina women, and breast cancer. One out of five Latina women in America carry the variant gene and about 1% carry two copies of the gene. While the real purpose of the gene is unknown, it was found that women who possessed the gene had less dense breast tissue as was shown from their mammograms. Dense breast tissue can often lead to breast cancer in women. This breast tissue correlation leads scientists to believe that the gene may have something to do with the production of estrogen receptors. According to Marc Hurlbert, the executive director of the Avon Foundation Breast Cancer Crusade, it is very important for them to discover what the gene actually does because it could lead to possible treatments for those who already have breast cancer.

In America, Latinas have the lowest risk for breast cancer when compared to African Americans and non-Hispanic whites. There are behavioral patterns that could also reduce the risk of breast cancer. Not using postmenopausal hormones and having more children at a younger age are both practiced by many Latina women and also reduce one’s risk for breast cancer. It is known now that there is also a genetic variant. After much research and looking at many genomes of breast cancer patients, geneticists discovered the location of the gene on the chromosome. On chromosome 6, a little SNP (single nucleotide polymorphism) was found to be the protective variant. Scientists were able to track the gene, not only to its location on genome, but to its indigenous ancestry. The gene could be found in 15% of Mexico, 10% in Columbia, and 5% in Puerto Rico, while its frequency was only found to be 1% in whites and blacks and about 2% of Chinese.

I find it really interesting that one simple gene could track itself through a nationality and have almost a direct correlation with breast cancer. Now that the gene has been located on chromosome 6, it might be able to be isolated and perhaps even put into use for the fight against breast cancer. It is understood that this gene does not mean the ultimate end to breast cancer. Dr. Otis W. Brawley reminds us of that saying, “…keep in mind that some women with this variant still get breast cancer.” What Dr. Brawley says next that perhaps this is because they have something that is cancelling this out. I would find it very interesting to look deeper into this possibility and see if there is in fact another gene that is inhibiting the SNP found on chromosome 6. Dr. Brawley also gives us hope saying, “I’m confident that this finding is going to hold, that most women who have this genetic variant are at lower risk for breast cancer.” I believe it would be amazing if this little SNP could be used to help so many people suffering from this terrible cancer.

http://well.blogs.nytimes.com/2014/10/20/genetic-variant-may-shield-latinas-from-breast-cancer/?_php=true&_type=blogs&module=Search&mabReward=relbias%3As%2C%7B%222%22%3A%22RI%3A12%22%7D&_r=0

Location on Human Genome Now Associated With Memory

With a recent analysis of genomic data and memory test results of over 14,000 older adults a location of the human genome has been identified to relate to better memory performance which was not associated with brain performance before. The gene known as FASTKD2, located on chromosome 2, revealed that better episodic memory resulted from a G nucleotide rather than the common A nucleotide. This change known as a single nucleotide polymorphism was also connected to a larger hippocampus, a brain structure involved with storing and retrieving memory, and increased gray dense matter in the brain on magnetic resonance imaging scans.

Although, there is no claim that this is the gene which is solely responsible for memory but the hopes of this information is that the FASTKD2 gene could be targeted to help those with conditions such as Alzheimer's disease. A decline in memory and hippocampal atrophy are two of the main symptoms which are associated with Alzheimer's therefore the correction of those symptoms by targeting the FASTKD2 gene is where research is now heading.

This was especially interesting to me because it is a new, and genetic, solution to attempting to treat Alzheimer's. There have been a lot of suggestions of what can help prevent or prolong the effects of Alzheimer's but now with a new approach there is an attempt to help treat as well. I also just found it intriguing that memory could be found to be associated with a specific gene, although it is not a single gene responsible for memory.
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